pkglint -r --network --only "migrate"
As a side-effect of migrating the homepages, pkglint also fixed a few
indentations in unrelated lines. These and the new homepages have been
checked manually.
pkglint --only "https instead of http" -r -F
With manual adjustments afterwards since pkglint 19.4.4 fixed a few
indentations in unrelated lines.
This mainly affects projects hosted at SourceForce, as well as
freedesktop.org, CTAN and GNU.
Upstream changelog
==================
Open Babel 3.0.0
@ghutchis ghutchis released this on 10 Oct - 29 commits to master since this release
This release represents a major update and is strongly recommended for all users.
It also removes deprecated components and breaks the API in a few places. For information on migrating from the previous version, please see:
https://open-babel.readthedocs.io/en/latest/UseTheLibrary/migration.html#migrating-to-3-0
We intend to move to semi-annual releases in Spring and Fall, with bug fix releases as needed.
A sample of major new features:
Code for handling implicit hydrogens and kekulization has been entirely replaced. As well as being accurate, the new approach is much faster.
Speed of reading and writing SMILES has been improved by more than 50-fold.
Removal of the old 'babel' binary in favor of the newer 'obabel' command-line tool.
New improved fragment-based 3D coordinate generation code as part of Google Summer of code 2018/2019. Significantly faster and more accurate: https://doi.org/10.1186/s13321-019-0372-5
(Please cite J. Cheminf. (2019) v11, article 49 if you use the new 3D coordinate generation.)
New API for handling reactions stored as molecules (e.g. Reaction InChI, etc.)
New API for copying part of an OBMol as a substructure
Support for Maestro file format, contributed by Patrick Lorton of Schrodinger
There are an incredible number of improvements, minor features and many bug fixes.
For a full list of changes and to download source packages (and eventually binaries)
https://open-babel.readthedocs.io/en/latest/ReleaseNotes/ob300.htmlhttps://github.com/openbabel/openbabel/releases
Thanks to a cast of many for this release, particularly including Noel O'Boyle;
aandi, adalke (Andrew Dalke), adamjstewart (Adam J. Stewart), afonari (Alexandr Fonari), artoria2e5 (Mingye Wang), baoilleach (Noel O'Boyle), barrymoo (Barry Moore), bbucior (Ben Bucior), boryszef (Borys Szefczyk), camannguyen (An Nguyen), cmanion (Charles A. Manion), cowsandmilk (David Hall), cstein (Casper Steinmann), derekharmon (Derek Harmon), djhogan (Daniel Hogan), dkoes (David Koes), e-kwsm (Eisuke Kawashima), eloyfelix (Eloy Felix), fredrikw (Fredrik Wallner), ghutchis (Geoff Hutchison), hille721 (Christoph Hille), hseara (Hector Martinez-Seara), jasonychuang (Jason Huang), jeffjanes (Jeff Janes), johnmay (John Mayfield), katrinleinweber (Katrin Leinweber), keipertk (Kristopher Keipert), kyle-roberts-arzeda, langner (Karol M. Langner), lorton (Pat Lorton), mcs07 (Matt Swain), merkys (Andrius Merkys), mkrykunov, mmghahremanpour (Mohammad Ghahremanpour), mwojcikowski (Maciej Wojcikowski), n-yoshikawa (Naruki Yoshikawa), nakatamaho (Nakata Maho), nsoranzo (Nicola Soranzo), oititov (Titov Oleg), orex (Kirill Okhotnikov), pbecherer (Paul Becherer), peawagon (Jen), philthiel (Philipp Thiel), psavery (Patrick Avery), rmeli (Rocco Meli), serval2412 (Julien Nabet), sunoru, susilehtola (Susi Lehtola), tgaudin (Theophile Gaudin), theavey (Thomas Heavey), timvdm (Tim Vandermeersch), torcolvin (Tor Colvin), wojdyr (Marcin Wojdyr), xomachine (Dmitriy Fomichev), yishutu (Yi-Shu Tu)
Open Babel 2.4.0 (2016-9-21)
This release represents a major update and should be a stable upgrade, strongly recommended for all users.
Note that this release deprecates the babel executable in favor of obabel. A future release will remove babel entirely. For information on the differences, please see the documentation.
New file formats
DALTON output files (read only) and DALTON input files (read/write) (Casper Steinmann)
JSON format used by ChemDoodle (read/write) (Matt Swain)
JSON format used by PubChem (read/write) (Matt Swain)
LPMD's atomic configuration file (read/write) (Joaquin Peralta)
The format used by the CONTFF and POSFF files in MDFF (read/write) (Kirill Okhotnikov)
ORCA output files (read only) and ORCA input files (write only) (Dagmar Lenk)
ORCA-AICCM's extended XYZ format (read/write) (Dagmar Lenk)
Painter format for custom 2D depictions (write only) (Noel O'Boyle)
Siesta output files (read only) (Patrick Avery)
Smiley parser for parsing SMILES according to the OpenSMILES specification (read only) (Tim Vandermeersch)
STL 3D-printing format (write only) (Matt Harvey)
Turbomole AOFORCE output (read only) (Mathias Laurin)
A representation of the VDW surface as a point cloud (write only) (Matt Harvey)
New file format capabilities and options
AutoDock PDBQT: Options to preserve hydrogens and/or atom names (Matt Harvey)
CAR: Improved space group support in .car files (kartlee)
CDXML: Read/write isotopes (Roger Sayle)
CIF: Extract charges (Kirill Okhotnikov)
CIF: Improved support for space-groups and symmetries (Alexandr Fonari)
DL_Poly: Cell information is now read (Kirill Okhotnikov)
Gaussian FCHK: Parse alpha and beta orbitals (Geoff Hutchison)
Gaussian out: Extract true enthalpy of formation, quadrupole, polarizability tensor, electrostatic potential fitting points and potential values, and more (David van der Spoel)
MDL Mol: Read in atom class information by default and optionally write it out (Roger Sayle)
MDL Mol: Support added for ZBO, ZCH and HYD extensions (Matt Swain)
MDL Mol: Implement the MDL valence model on reading (Roger Sayle)
MDL SDF: Option to write out an ASCII depiction as a property (Noel O'Boyle)
mmCIF: Improved mmCIF reading (Patrick Fuller)
mmCIF: Support for atom occupancy and atom_type (Kirill Okhotnikov)
Mol2: Option to read UCSF Dock scores (Maciej Wojcikowski)
MOPAC: Read z-matrix data and parse (and prefer) ESP charges (Geoff Hutchison)
NWChem: Support sequential calculations by optionally overwriting earlier ones (Dmitriy Fomichev)
NWChem: Extract info on MEP(IRC), NEB and quadrupole moments (Dmitriy Fomichev)
PDB: Read/write PDB insertion codes (Steffen Moller)
PNG: Options to crop the margin, and control the background and bond colors (Fredrik Wallner)
PQR: Use a stored atom radius (if present) in preference to the generic element radius (Zhixiong Zhao)
PWSCF: Extend parsing of lattice vectors (David Lonie)
PWSCF: Support newer versions, and the 'alat' term (Patrick Avery)
SVG: Option to avoid addition of hydrogens to fill valence (Lee-Ping)
SVG: Option to draw as ball-and-stick (Jean-Noel Avila)
VASP: Vibration intensities are calculated (Christian Neiss, Mathias Laurin)
VASP: Custom atom element sorting on writing (Kirill Okhotnikov)
Other new features and improvements
2D layout: Improved the choice of which bonds to designate as hash/wedge bonds around a stereo center (Craig James)
3D builder: Use bond length corrections based on bond order from Pyykko and Atsumi (http://dx.doi.org/10.1002/chem.200901472) (Geoff Hutchison)
3D generation: "--gen3d", allow user to specify the desired speed/quality (Geoff Hutchison)
Aromaticity: Improved detection (Geoff Hutchison)
Canonicalisation: Changed behaviour for multi-molecule SMILES. Now each molecule is canonicalized individually and then sorted. (Geoff Hutchison/Tim Vandermeersch)
Charge models: "--print" writes the partial charges to standard output after calculation (Geoff Hutchison)
Conformations: Confab, the systematic conformation generator, has been incorporated into Open Babel (David Hall/Noel O'Boyle)
Conformations: Initial support for ring rotamer sampling (Geoff Hutchison)
Conformer searching: Performance improvement by avoiding gradient calculation and optimising the default parameters (Geoff Hutchison)
EEM charge model: Extend to use additional params from http://dx.doi.org/10.1186/s13321-015-0107-1 (Tomas Racek)
FillUnitCell operation: Improved behavior (Patrick Fuller)
Find duplicates: The "--duplicate" option can now return duplicates instead of just removing them (Chris Morley)
GAFF forcefield: Atom types updated to match Wang et al. J. Comp. Chem. 2004, 25, 1157 (Mohammad Ghahremanpour)
New charge model: EQeq crystal charge equilibration method (a speed-optimized crystal-focused charge estimator, http://pubs.acs.org/doi/abs/10.1021/jz3008485) (David Lonie)
New charge model: "fromfile" reads partial charges from a named file (Matt Harvey)
New conversion operation: "changecell", for changing cell dimensions (Kirill Okhotnikov)
New command-line utility: "obthermo", for extracting thermochemistry data from QM calculations (David van der Spoel)
New fingerprint: ECFP (Geoff Hutchison/Noel O'Boyle/Roger Sayle)
OBConversion: Improvements and API changes to deal with a long-standing memory leak (David Koes)
OBAtom::IsHBondAcceptor(): Definition updated to take into account the atom environment (Stefano Forli)
Performance: Faster ring-finding algorithm (Roger Sayle)
Performance: Faster fingerprint similarity calculations if compiled with -DOPTIMIZE_NATIVE=ON (Noel O'Boyle/Jeff Janes)
SMARTS matching: The "-s" option now accepts an integer specifying the number of matches required (Chris Morley)
UFF: Update to use traditional Rappe angle potential (Geoff Hutchison)
Language bindings
Bindings: Support compiling only the bindings against system libopenbabel (Reinis Danne)
Java bindings: Add example Scala program using the Java bindings (Reinis Danne)
New bindings: PHP (Maciej Wojcikowski)
PHP bindings: BaPHPel, a simplified interface (Maciej Wojcikowski)
Python bindings: Add 3D depiction support for Jupyter notebook (Patrick Fuller)
Python bindings, Pybel: calccharges() and convertdbonds() added (Patrick Fuller, Bjorn Gruning)
Python bindings, Pybel: compress output if filename ends with .gz (Maciej Wojcikowski)
Python bindings, Pybel: Residue support (Maciej Wojcikowski)
Development/Build/Install Improvements
Version control: move to git and GitHub from subversion and SourceForge
Continuous integration: Travis for Linux builds and Appveyor for Windows builds (David Lonie and Noel O'Boyle)
Python installer: Improvements to the Python setup.py installer and "pip install openbabel" (David Hall, Matt Swain, Joshua Swamidass)
Compilation speedup: Speed up compilation by combining the tests (Noel O'Boyle)
MacOSX: Support compiling with libc++ on MacOSX (Matt Swain)
Cast of contributors
Alexandr Fonari, Anders Steen Christensen, Andreas Kempe, arkose, Benoit Leblanc, Bjorn Gruning, Casper Steinmann, Chris Morley, Christoph Willing, Craig James, Dagmar Lenk, David Hall, David Koes, David Lonie, David van der Spoel, Dmitriy Fomichev, Fulvio Ciriaco, Fredrik Wallner, Geoff Hutchison, Heiko Becker, Itay Zandbank, Jean-Noel Avila, Jeff Janes, Joaquin Peralta, Joshua Swamidass, Julien Nabet, Karol Langner, Karthik Rajagopalan, Katsuhiko Nishimra, Kevin Horan, Kirill Okhotnikov, Lee-Ping, Matt Harvey, Maciej Wojcikowski, Marcus Hanwell, Mathias Laurin, Matt Swain, Mohamad Mohebifar, Mohammad Ghahremanpour, Noel O'Boyle, Patrick Avery, Patrick Fuller, Paul van Maaren, Peng Bai, Philipp Thiel, Reinis Danne, Roger Sayle, Ronald Cohen, Scott McKechnie, Stefano Forli, Steve Roughley, Steffen Moeller, Tim Vandermeersch, Tomas Racek, Tomas Trnka, Tor Colvin, Torsten Sachse, Yi-Shu Tu, Zhixiong Zhao
Start building FreeGLUT with GLUT compatibility on.
- GLUT's maintainance state is much worse than FreeGLUT's, with no
substanital commits since 2011.
- GLUT can no longer be consider a core component of Mesa or X11.
- Nobody except us seems to be using it...
Other vendors still shipping GLUT:
- GoboLinux, T2 SDE, PLD Linux
Revbump packages using GLUT or freeglut by default.
The biopython license is _very_ similar, but not identical, to many
other open source licenses used throughout pkgsrc. The gratuitous
differences are being addressed by the project through an effort to
relicense all files to the 3-clause BSD license. In the meantime,
Debian has accepted that the current biopython license meets the DFSG
and includes the package in their main distribution. Consequently,
rename the license file and add it to DEFAULT_ACCEPTABLE_LICENSES.
See http://mail-index.netbsd.org/pkgsrc-changes/2019/08/13/msg195804.html.
The Biopython package contains high-quality, reusable modules and
scripts written in Python to make it as easy as possible to use Python
for bioinformatics. The Biopython includes the follwing: the ability
to parse bioinformatics files into python utilizable data structures,
including support for the formats such as Blast output, Clustalw,
FASTA, GenBank, PubMed and Medicine, various Expasy files, SCOP,
Rebase, UniGene, and SwissProt.
VSEARCH supports de novo and reference based chimera detection,
clustering, full-length and prefix dereplication, rereplication,
reverse complementation, masking, all-vs-all pairwise global
alignment, exact and global alignment searching, shuffling,
subsampling and sorting. It also supports FASTQ file analysis,
filtering, conversion and merging of paired-end reads.
The aim of this project is to create an alternative to the USEARCH
tool developed by Robert C. Edgar (2010).
fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
Upstream build does not use LDFLAGS canonically.
Makefile.in will require restructuring to eliminate workaround.
This patch fixes build on CentOS and build with RELRO on NetBSD.
Also add LICENSE and fig2dev runtime dependency.
HISAT2 is a fast and sensitive alignment program for mapping next-generation
sequencing reads (both DNA and RNA) to a population of human genomes (as well
as to a single reference genome).
Canu is a fork of the Celera Assembler, designed for high-noise single-molecule
sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
Canu is a hierarchical assembly pipeline which runs in four steps:
Detect overlaps in high-noise sequences using MHAP
Generate corrected sequence consensus
Trim corrected sequences
Assemble trimmed corrected sequences
